End-sequence profiling: Sequence-based analysis of aberrant genomes
End-sequence profiling: Sequence-based analysis of aberrant genomes
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DOI：
10.1073/pnas.1232418100
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发表时间：
2003-06-24
影响因子：
11.1
通讯作者：
Collins, C
中科院分区：
文献类型：
--
作者：
Volik, S;Zhao, SY;Collins, C
基因组重排在进化、癌症和其他疾病中都很重要。重排的精确定位对于识别相关基因至关重要，为此已经开发了许多技术。我们在这里展示了末端序列分析（ESP）特别适合于这一目的。ESP是通过从测试基因组构建细菌人工染色体（BAC）文库，测量BAC末端序列，并将末端序列对映射到正常基因组序列来完成的。BAC端序列密度图以高分辨率识别拷贝数异常。跨越结构畸变的BACs在正常基因组序列上具有异常远的端对。然后可以对这些对进行测序，以确定所涉及的基因和断点序列。乳腺癌细胞系MCF-7的ESP分析证明了其在复杂基因组分析中的实用性。对近8000个克隆（0.37倍单倍体基因组克隆覆盖率）进行末端测序，得到了分辨率超过300 kb的MCF-7基因组拷贝数图谱，鉴定出381个基因组断点，其中一个子集通过荧光原位杂交图谱和测序进行了验证。
Genome rearrangements are important in evolution, cancer, and other diseases. Precise mapping of the rearrangements is essential for identification of the involved genes, and many techniques have been developed for this purpose. We show here that end-sequence profiling (ESP) is particularly well suited to this purpose. ESP is accomplished by constructing a bacterial artificial chromosome (BAC) library from a test genome, measuring BAC end sequences, and mapping end-sequence pairs onto the normal genome sequence. Plots of BAC end-sequences density identify copy number abnormalities at high resolution. BACs spanning structural aberrations have end pairs that map abnormally far apart on the normal genome sequence. These pairs can then be sequenced to determine the involved genes and breakpoint sequences. ESP analysis of the breast cancer cell line MCF-7 demonstrated its utility for analysis of complex genomes. End sequencing of approximate to8,000 clones (0.37-fold haploid genome clonal coverage) produced a comprehensive genome copy number map of the MCF-7 genome at better than 300-kb resolution and identified 381 genome breakpoints, a subset of which was verified by fluorescence in situ hybridization mapping and sequencing.